ABIO docs

ABIO Topics

Cross-cutting topics that span multiple subsystems.

A

• ABIO DAT - dvc_dat integration, name resolution, _spec_.yaml format
• Agent Interface - Agent protocol, LLM bindings, API key management, experiment lifecycle
• Alien Vocabulary - Naming conventions for alien biology elements
• alienbio - Top-level module: do, create, load, save, parse, ctx, o

B

• Bio - Higher-level biology interface: fetch, store, expand, sim, run
• [[Bio CLI]] - Command-line interface: bio report, bio run, bio generate

C

• Catalog Naming Scheme - Standard naming for catalog biological entity templates

D

• Decorators - Python decorators: @biotype, @fn, @scoring, @action, @measurement, @rate
• Documentation - Documentation standards and conventions

G

• [[Generator Spec Language]] - YAML syntax for scenario generator specs and templates

R

• [[ABIO Roadmap]] - Generator implementation roadmap (templates, expansion, guards, visibility)

S

• [[Skinning]] - See Generator Spec#Visibility Specification — presenting scenarios with different name mappings (transparent vs opaque)
• [[Spec Language]] - YAML syntax: typed elements, evaluation constructs, defaults inheritance

T

• Testing - Testing tiers (smoke, commit, release), test organization

V

• [[Visibility]] - See [[Skinning]], Generator Spec#Visibility Specification — what the AI can observe, name mapping